[galaxy-commits] commit/galaxy-central: james_taylor: template: Move templates used only by the galaxy webapp into templates/webapps/galaxy

3 Feb 2013

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/4c6e63dc04c9/
changeset:   4c6e63dc04c9
user:        james_taylor
date:        2013-02-04 05:07:11
summary:     template: Move templates used *only* by the galaxy webapp into templates/webapps/galaxy
affected #:  258 files

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/cloud/index.mako

--- a/templates/cloud/index.mako
+++ /dev/null
@@ -1,291 +0,0 @@
-<%inherit file="/webapps/galaxy/base_panels.mako"/>
-
-<%def name="init()">
-<%
-    self.has_left_panel=False
-    self.has_right_panel=False
-    self.active_view="shared"
-    self.message_box_visible=False
-%>
-</%def>
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "autocomplete_tagging" )}
-    <style type="text/css">
-    #new_history_p{
-        line-height:2.5em;
-        margin:0em 0em .5em 0em;
-    }
-    #new_history_cbx{
-        margin-right:.5em;
-    }
-    #new_history_input{
-        display:none;
-        line-height:1em;
-    }
-    #ec_button_container{
-        float:right;
-    }
-    #hidden_options{
-        display:none;
-    }
-    div.toolForm{
-        margin-top: 10px;
-        margin-bottom: 10px;
-    }
-    div.toolFormTitle{
-        cursor:pointer;
-    }
-    .title_ul_text{
-        text-decoration:underline;
-    }
-    .step-annotation {
-        margin-top: 0.25em;
-        font-weight: normal;
-        font-size: 97%;
-    }
-    .workflow-annotation {
-        margin-bottom: 1em;
-    }
-    #loading_indicator{
-            position:fixed;
-            top:40px;
-    }
-    </style>
-</%def>
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-    <script type="text/javascript">
-        var ACCOUNT_URL = "${h.url_for( controller='/cloudlaunch', action='get_account_info')}";
-        var PKEY_DL_URL = "${h.url_for( controller='/cloudlaunch', action='get_pkey')}";
-        var cloudlaunch_clusters = [];
-
-        $(document).ready(function(){
-            $('#id_existing_instance').change(function(){
-                var ei_name = $(this).val();
-                if (ei_name === "New Cluster"){
-                    //For new instances, need to see the cluster name field.
-                    $('#id_cluster_name').val("New Cluster")
-                    $('#cluster_name_wrapper').show('fast');
-                }else{
-                    //Hide the Cluster Name field, but set the value
-                    $('#id_cluster_name').val($(this).val());
-                    $('#cluster_name_wrapper').hide('fast');
-                }
-            });
-             //When id_secret and id_key are complete, submit to get_account_info
-            $("#id_secret, #id_key_id").bind("paste input propertychange", function(){
-                secret_el = $("#id_secret");
-                key_el = $("#id_key_id");
-                if (secret_el.val().length === 40 && key_el.val().length === 20){
-                    //Submit these to get_account_info, unhide fields, and update as appropriate
-                    $.ajax({type: "POST",
-                            url: ACCOUNT_URL,
-                            dataType: 'json',
-                            data: {key_id: key_el.val(),secret:secret_el.val()},
-                            success: function(result){
-                                    cloudlaunch_clusters = result.clusters;
-                                    var kplist = $("#id_keypair");
-                                    var clusterlist = $("#id_existing_instance");
-                                    kplist.find('option').remove();
-                                    clusterlist.find('option').remove();
-                                    //Update fields with appropriate elements
-                                    clusterlist.append($('<option/>').val('New Cluster').text('New Cluster'));
-                                    if (_.size(result.clusters) > 0){
-                                        _.each(result.clusters, function(cluster, index){
-                                            clusterlist.append($('<option/>').val(cluster.name).text(cluster.name));
-                                        });
-                                        $('#existing_instance_wrapper').show();
-                                    }
-                                    if (!_.include(result.keypairs, '${default_keypair}')){
-                                        kplist.append($('<option/>').val('${default_keypair}').text('Create New - ${default_keypair}'));
-                                    }
-                                    _.each(result.keypairs, function(keypair, index){
-                                        kplist.append($('<option/>').val(keypair).text(keypair));
-                                    });
-                                    $('#hidden_options').show('fast');
-                                }
-                            });
-                }
-            });
-            $('#loading_indicator').ajaxStart(function(){
-                $(this).show('fast');
-            }).ajaxStop(function(){
-                $(this).hide('fast');
-            });
-            $('form').ajaxForm({
-                    type: 'POST',
-                    dataType: 'json',
-                    beforeSubmit: function(data, form){
-                        if ($('#id_password').val() != $('#id_password_confirm').val()){
-                            //Passwords don't match.
-                            form.prepend('<div class="errormessage">Passwords do not match</div>');
-                            return false;
-                        }else{
-                            //Clear errors
-                            $('.errormessage').remove()
-                            //Hide the form, show pending box with spinner.
-                            $('#launchFormContainer').hide('fast');
-                            $('#responsePanel').show('fast');
-                        }
-                        //Dig up zone info for selected cluster, set hidden input.
-                        //This is not necessary to present to the user though the interface may prove useful.
-                        var ei_val = _.find(data, function(f_obj){return f_obj.name === 'existing_instance'});
-                        if( ei_val && (ei_val.value !== "New Cluster")){
-                            var cluster = _.find(cloudlaunch_clusters, function(cluster){return cluster.name === ei_val.value});
-                            var zdata = _.find(data, function(f_obj){return f_obj.name === 'zone'});
-                            zdata.value = cluster.zone;
-                        }
-                    },
-                    success: function(data){
-                        //Success Message, link to key download if required, link to server itself.
-                        $('#launchPending').hide('fast');
-                        //Set appropriate fields (dns, key, ami) and then display.
-                        if(data.kp_material_tag){
-                            var kp_download_link = $('<a/>').attr('href', PKEY_DL_URL + '?kp_material_tag=' + data.kp_material_tag)
-                                                            .attr('target','_blank')
-                                                            .text("Download your key now");
-                            $('#keypairInfo').append(kp_download_link);
-                            $('#keypairInfo').show();
-                        }
-                        $('.kp_name').text(data.kp_name);
-                        $('#instance_id').text(data.instance_id);
-                        $('#image_id').text(data.image_id);
-                        $('#instance_link').html($('<a/>')
-                            .attr('href', 'http://' + data.public_dns_name + '/cloud')
-                            .attr('target','_blank')
-                            .text(data.public_dns_name + '/cloud'));
-                        $('#instance_dns').text(data.public_dns_name);
-                        $('#launchSuccess').show('fast');
-                    },
-                    error: function(jqXHR, textStatus, errorThrown){
-                       $('#launchFormContainer').prepend('<div class="errormessage">' + errorThrown + " : " + jqXHR.responseText + '</div>');
-                       $('#responsePanel').hide('fast');
-                       $('#launchFormContainer').show('fast');
-                    }
-            });
-        });
-    </script>
-</%def>
-
-<%def name="center_panel()">
-    <div style="overflow: auto; height: 100%;">
-        <div class="page-container" style="padding: 10px;">
-        <div id="loading_indicator"></div>
-            <h2>Launch a Galaxy Cloud Instance</h2>
-              <div id="launchFormContainer" class="toolForm">
-                    <form id="cloudlaunch_form" action="${h.url_for( controller='/cloudlaunch', action='launch_instance')}" method="post">
-
-                    <p>To launch a Galaxy Cloud Cluster, enter your AWS Secret Key ID, and Secret Key.  Galaxy will use
-                    these to present appropriate options for launching your cluster.   Note that using this form to
-                    launch computational resources in the Amazon Cloud will result in   costs to the account indicated
-                    above.  See <a href="http://aws.amazon.com/ec2/pricing/">Amazon's pricing</a> for more information.
-                    options for launching your cluster.</p></p>
-
-                    <div class="form-row">
-                        <label for="id_key_id">Key ID</label>
-                        <input type="text" size="30" maxlength="20" name="key_id" id="id_key_id" value=""/><br/>
-                        <div class="toolParamHelp">
-                            This is the text string that uniquely identifies your account, found in the 
-                            <a href="https://portal.aws.amazon.com/gp/aws/securityCredentials">Security Credentials section of the AWS Console</a>.
-                        </div>
-                    </div>
-
-                    <div class="form-row">
-                        <label for="id_secret">Secret Key</label>
-                        <input type="text" size="50" maxlength="40" name="secret" id="id_secret" value=""/><br/>
-                        <div class="toolParamHelp">
-                            This is your AWS Secret Key, also found in the <a href="https://portal.aws.amazon.com/gp/aws/securityCredentials">Security
-Credentials section of the AWS Console</a>.  </div>
-                    </div>
-
-                    <div id="hidden_options">
-                        <div id='existing_instance_wrapper' style="display:none;" class="form-row">
-                                <label for="id_existing_instance">Instances in your account</label>
-                                <select name="existing_instance" id="id_existing_instance">
-                                </select>
-                                <input id='id_zone' type='hidden' name='zone' value=''/>
-                        </div>
-                        <div id='cluster_name_wrapper' class="form-row">
-                            <label for="id_cluster_name">Cluster Name</label>
-                            <input type="text" size="40" class="text-and-autocomplete-select" name="cluster_name" id="id_cluster_name"/><br/>
-                            <div class="toolParamHelp">
-                                This is the name for your cluster.  You'll use this when you want to restart.
-                            </div>
-                        </div>
-
-                        <div class="form-row">
-                            <label for="id_password">Cluster Password</label>
-                            <input type="password" size="40" name="password" id="id_password"/><br/>
-                        </div>
-
-                        <div class="form-row">
-                            <label for="id_password_confirm">Cluster Password - Confirmation</label>
-                            <input type="password" size="40" name="password_confirm" id="id_password_confirm"/><br/>
-                        </div>
-
-
-                        <div class="form-row">
-                            <label for="id_keypair">Key Pair</label>
-                            <select name="keypair" id="id_keypair">
-                                <option name="Create" value="cloudman_keypair">cloudman_keypair</option>
-                            </select>
-                        </div>
-
-                        %if share_string:
-                            <input type='hidden' name='share_string' value='${share_string}'/>
-                        %else:
-                        <!-- DBEDIT temporary hide share string due to it being broken on the cloudman end -->
-                        <div class="form-row" style="display:none;">
-                            <label for="id_share_string">Instance Share String (optional)</label>
-                            <input type="text" size="120" name="share_string" id="id_share_string"/><br/>
-                        </div>
-                        %endif
-
-                        <div class="form-row">
-                            <label for="id_instance_type">Instance Type</label>
-                            <select name="instance_type" id="id_instance_type">
-                                <option value="m1.large">Large</option>
-                                <option value="m1.xlarge">Extra Large</option>
-                                <option value="m2.4xlarge">High-Memory Quadruple Extra Large</option>
-                            </select>
-                        </div>
-                        <div class="form-row">
-                            <p>Requesting the instance may take a moment, please be patient.  Do not refresh your browser or navigate away from the page</p>
-                            <input type="submit" value="Submit" id="id_submit"/>
-                        </div>
-                    </div>
-                        <div class="form-row">
-                        <div id="loading_indicator" style="position:relative;left:10px;right:0px"></div>
-                        </div>
-                    </form>
-                </div>
-                <div id="responsePanel" class="toolForm" style="display:none;">
-                        <div id="launchPending">Launch Pending, please be patient.</div>
-                        <div id="launchSuccess" style="display:none;">
-                            <div id="keypairInfo" style="display:none;margin-bottom:20px;">
-                                <h3>Very Important Key Pair Information</h3>
-                                <p>A new key pair named <strong><span class="kp_name">kp_name</span></strong> has been created in your AWS
-                                account and will be used to access this instance via ssh. It is
-                                <strong>very important</strong> that you save the following private key
-                                as it is not saved on this Galaxy instance and will be permanently lost if not saved.  Additionally, this link will
-                                only allow a single download, after which the key is removed from the Galaxy server permanently.<br/>
-                            </div>
-                            <div>
-                                <h3>Access Information</h3>
-                                <ul>
-                                    <li>Your instance '<span id="instance_id">undefined</span>' has been successfully launched using the
-                                '<span id="image_id">undefined</span>' AMI.</li>
-                                <li>While it may take a few moments to boot, you will be able to access the cloud control
-                                panel at <span id="instance_link">undefined.</span>.</li>
-                            <li>SSH access is also available using your private key.  From the terminal, you would execute something like:</br>    `ssh -i <span class="kp_name">undefined</span>.pem ubuntu@<span
-id="instance_dns">undefined</span>`</li>
-                                </ul>
-                        </div>
-                </div>
-        </div>
-    </div>
-</%def>
-

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/cloud/run.mako
--- a/templates/cloud/run.mako
+++ /dev/null
@@ -1,41 +0,0 @@
-<%inherit file="/webapps/galaxy/base_panels.mako"/>
-
-<%def name="init()">
-<%
-    self.has_left_panel=False
-    self.has_right_panel=False
-    self.active_view="shared"
-    self.message_box_visible=False
-%>
-</%def>
-
-
-<%def name="center_panel()">
-    <div style="overflow: auto; height: 100%;">
-        <div class="page-container" style="padding: 10px;">
-            <h2>Launching a Galaxy Cloud Instance</h2>
-%if error:
-    <p>${error}</p>
-%elif instance:
-    %if kp_material:
-        <h3>Very Important Key Pair Information</h3>
-        <p>A new key pair named '${kp_name}' has been created in your AWS
-        account and will be used to access this instance via ssh. It is
-        <strong>very important</strong> that you save the following private key
-        as it is not saved on this Galaxy instance and will be permanently lost
-        once you leave this page.  To do this, save the following key block as
-        a plain text file named '${kp_name}'.</p>
-        <pre>${kp_material}</pre>
-    %endif
-    <p>The instance '${instance.id} has been successfully launched using the
-    '${instance.image_id}' AMI.<br/>  Access it at <a
-    href="http://${instance.public_dns_name}">http://${instance.public_dns_name}</a></p>
-    <p>SSH access is available using your private key '${kp_name}'.</p>
-%else:
-    <p> Unknown failure, no instance.  Please refer to your AWS console at <a
-    href="https://console.aws.amazon.com">https://console.aws.amazon.com</a></p>
-%endif
-        </div>
-    </div>
-</%def>
-

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/copy_view.mako
--- a/templates/dataset/copy_view.mako
+++ /dev/null
@@ -1,141 +0,0 @@
-<%inherit file="/base.mako"/>
-<%def name="title()">Copy History Items</%def>
-
-<%def name="javascripts()">
-
-    ${parent.javascripts()}
-    
-    <script type="text/javascript">
-        $(function() {
-            $("#select-multiple").click(function() {
-                $("#single-dest-select").val("");
-                $("#single-destination").hide();
-                $("#multiple-destination").show();
-            });
-        });
-        %if 'history' in refresh_frames:
-            if ( parent.frames && parent.frames.galaxy_history ) {
-                parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}";
-                if ( parent.force_right_panel ) {
-                    parent.force_right_panel( 'show' );
-                }
-            }
-        %endif
-    </script>
-    
-</%def>
-
-%if error_msg:
-    <p>
-        <div class="errormessage">${error_msg}</div>
-        <div style="clear: both"></div>
-    </p>
-%endif
-%if done_msg:
-    <p>
-        <div class="donemessage">${done_msg}</div>
-        <div style="clear: both"></div>
-    </p>
-%endif
-<p>
-    <div class="infomessage">Copy any number of history items from one history to another.</div>
-    <div style="clear: both"></div>
-</p>
-<p>
-    <form method="post">
-        <div class="toolForm" style="float: left; width: 45%; padding: 0px;">
-            <div class="toolFormTitle">Source History:<br />
-                <select id="source_history" name="source_history" refresh_on_change="true" style="font-weight: normal;">
-                    %for i, hist in enumerate(target_histories):
-                        <%
-                            selected = ""
-                            current_history_text = ""
-                            if hist == source_history:
-                                selected = "selected='selected'"
-                            if hist == current_history:
-                                current_history_text = " (current history)"
-                            
-                        %>
-                        <option value="${trans.security.encode_id(hist.id)}" ${selected}>
-                            ${i + 1}: ${h.truncate(util.unicodify( hist.name ), 30)}${current_history_text}
-                        </option>
-                    %endfor
-                </select>
-            </div>
-            <div class="toolFormBody">
-                %if len(source_datasets) > 0:
-                    %for data in source_datasets:
-                        <%
-                            checked = ""
-                            encoded_id = trans.security.encode_id(data.id)
-                            if data.id in source_dataset_ids:
-                                checked = " checked='checked'"
-                        %>
-                        <div class="form-row">
-                            <input type="checkbox" name="source_dataset_ids" id="dataset_${encoded_id}" value="${encoded_id}"${checked}/>
-                            <label for="dataset_${encoded_id}" style="display: inline;font-weight:normal;"> ${data.hid}: ${h.to_unicode(data.name)}</label>
-                        </div>
-                    %endfor
-                %else:
-                    <div class="form-row">This history has no datasets.</div>
-                %endif
-            </div>
-        </div>
-        <div style="float: left; padding-left: 10px; font-size: 36px;">→</div>
-        <div class="toolForm" style="float: right; width: 45%; padding: 0px;">
-            <div class="toolFormTitle">Destination History:</div>
-            <div class="toolFormBody">
-                <div class="form-row" id="single-destination">
-                    <select id="single-dest-select" name="target_history_id">
-                        <option value=""></option>
-                        %for i, hist in enumerate(target_histories):
-                            <%
-                                encoded_id = trans.security.encode_id(hist.id)
-                                source_history_text = ""
-                                selected = ""
-                                if hist == source_history:
-                                    source_history_text = " (source history)"
-                                if encoded_id == target_history_id:
-                                    selected = " selected='selected'"
-                            %>
-                            <option value="${encoded_id}"${selected}>${i + 1}: ${h.truncate( util.unicodify( hist.name ), 30)}${source_history_text}</option>
-                        %endfor
-                    </select><br /><br />
-                    <a style="margin-left: 10px;" href="javascript:void(0);" id="select-multiple">Choose multiple histories</a>
-                </div>
-                <div id="multiple-destination" style="display: none;">
-                    %for i, hist in enumerate( target_histories ):
-                        <%
-                            cur_history_text = ""
-                            encoded_id = trans.security.encode_id(hist.id)
-                            if hist == source_history:
-                                cur_history_text = " <strong>(source history)</strong>"
-                        %>
-                        <div class="form-row">
-                            <input type="checkbox" name="target_history_ids" id="hist_${encoded_id}" value="${encoded_id}"/>
-                            <label for="hist_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${ util.unicodify( hist.name ) }${cur_history_text}</label>
-                        </div>
-                    %endfor
-                </div>
-                %if trans.get_user():
-                    <%
-                        checked = ""
-                        if "create_new_history" in target_history_ids:
-                            checked = " checked='checked'"
-                    %>
-                    <hr />
-                    <div style="text-align: center; color: #888;">— OR —</div>
-                    <div class="form-row">
-                        <label for="new_history_name" style="display: inline; font-weight:normal;">New history named:</label>
-                        <input type="textbox" name="new_history_name" />
-                    </div>
-                %endif
-            </div>
-        </div>
-            <div style="clear: both"></div>
-            <div class="form-row" align="center">
-                <input type="submit" class="primary-button" name="do_copy" value="Copy History Items"/>
-            </div>
-        </form>
-    </div>
-</p>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/display.mako
--- a/templates/dataset/display.mako
+++ /dev/null
@@ -1,111 +0,0 @@
-## Because HDAs do not have many of the properties that other sharable items have, we need to override most of the default code for display.
-<%inherit file="/display_base.mako"/>
-<%namespace file="/display_common.mako" import="*" />
-<%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" />
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-</%def>
-
-<%def name="init()">
-<%
-    self.has_left_panel=False
-    self.has_right_panel=True
-    self.message_box_visible=False
-    self.active_view="user"
-    self.overlay_visible=False
-%>
-</%def>
-
-<%def name="title()">
-    Galaxy | ${get_class_display_name( item.__class__ )} | ${get_item_name( item ) | h}
-</%def>
-
-<%def name="render_item_links( data )">
-    ## Provide links to save data and import dataset.
-    <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( data.id ), to_ext=data.ext )}" class="icon-button disk tooltip" title="Save dataset"></a>
-        <a 
-            href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( data.id ) )}"
-            class="icon-button import tooltip" 
-            title="Import dataset"></a>
-</%def>
-
-<%def name="render_item( data, data_to_render )">
-    %if truncated:
-        <div class="warningmessagelarge">
-            This dataset is large and only the first megabyte is shown below. | 
-            <a href="${h.url_for( controller='dataset', action='display_by_username_and_slug', username=data.history.user.username, slug=trans.security.encode_id( data.id ), preview=False )}">Show all</a>
-        </div>    
-    %endif
-    ## TODO: why is the default font size so small?
-    <pre style="font-size: 135%">${ data_to_render | h }</pre>
-</%def>
-
-
-<%def name="center_panel()">
-    <div class="unified-panel-header" unselectable="on">
-        <div class="unified-panel-header-inner">
-                ${get_class_display_name( item.__class__ )}
-            | ${get_item_name( item ) | h}
-        </div>
-    </div>
-    
-    <div class="unified-panel-body">
-        <div style="overflow: auto; height: 100%;">        
-            <div class="page-body">
-                <div style="float: right">
-                    ${self.render_item_links( item )}
-                </div>
-                <div>
-                    ${self.render_item_header( item )}
-                </div>
-                
-                ${self.render_item( item, item_data )}
-            </div>
-        </div>
-    </div>
-</%def>
-
-<%def name="right_panel()">
-    <div class="unified-panel-header" unselectable="on">
-        <div class="unified-panel-header-inner">
-            About this ${get_class_display_name( item.__class__ )}
-        </div>
-    </div>
-    
-    <div class="unified-panel-body">
-        <div style="overflow: auto; height: 100%;">
-            <div style="padding: 10px;">
-                <h4>Author</h4>
-                
-                <p>${item.history.user.username | h}</p>
-                
-                <div><img src="https://secure.gravatar.com/avatar/${h.md5(item.history.user.email)}?d=identicon&s=150"></div>
-
-                ## Page meta. 
-                
-                ## No links for datasets right now.
-        
-                ## Tags.
-                <p>
-                <h4>Tags</h4>
-                <p>
-                ## Community tags.
-                <div>
-                    Community:
-                    ${render_community_tagging_element( tagged_item=item, tag_click_fn='community_tag_click', use_toggle_link=False )}
-                    %if len ( item.tags ) == 0:
-                        none
-                    %endif
-                </div>
-                ## Individual tags.
-                <p>
-                <div>
-                    Yours:
-                    ${render_individual_tagging_element( user=trans.get_user(), tagged_item=item, elt_context='view.mako', use_toggle_link=False, tag_click_fn='community_tag_click' )}
-                </div>
-            </div>    
-        </div>
-    </div>
-
-</%def>
\ No newline at end of file

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/display_application/display.mako
--- a/templates/dataset/display_application/display.mako
+++ /dev/null
@@ -1,12 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%def name="title()">Display Application: ${display_link.link.display_application.name}  ${display_link.link.name}</%def>
-%for message, status in msg:
-    ${render_msg( message, status )}
-%endfor
-%if refresh:
-<%def name="metas()"><meta http-equiv="refresh" content="10" /></%def>
-<p>
-This page will <a href="${trans.request.url}">refresh</a> after 10 seconds.
-</p>
-%endif

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/edit_attributes.mako
--- a/templates/dataset/edit_attributes.mako
+++ /dev/null
@@ -1,202 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-<%namespace file="/message.mako" name="message_ns" import="handle_refresh_frames" />
-
-<%def name="title()">${_('Edit Dataset Attributes')}</%def>
-
-<%def name="stylesheets()">
-    ${h.css( "base", "autocomplete_tagging" )}
-</%def>
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-    ${message_ns.handle_refresh_frames()}
-    ${h.js( "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )}
-</%def>
-
-<%def name="datatype( dataset, datatypes )">
-    <select name="datatype">
-        %for ext in datatypes:
-            %if dataset.ext == ext:
-                <option value="${ext}" selected="yes">${_(ext)}</option>
-            %else:
-                <option value="${ext}">${_(ext)}</option>
-            %endif
-        %endfor
-    </select>
-</%def>
-
-%if message:
-    ${render_msg( message, status )}
-%endif
-
-
-<ul class="nav nav-tabs">
-    <li class="active"><a href="#attributes" data-toggle="tab">Attributes</a></li>
-    <li><a href="#convert" data-toggle="tab">Convert Format</a></li>
-    <li><a href="#datatype" data-toggle="tab">Datatype</a></li>
-    <li><a href="#permissions" data-toggle="tab">Permissions</a></li>
-</ul>
-
-<div class="tab-content">
-
-<div class="tab-pane active toolForm" id="attributes">
-    <div class="toolFormTitle">${_('Edit Attributes')}</div>
-    <div class="toolFormBody">
-        <form name="edit_attributes" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post">
-            <div class="form-row">
-                <label>
-                    Name:
-                </label>
-                <div style="float: left; width: 250px; margin-right: 10px;">
-                    <input type="text" name="name" value="${data.get_display_name() | h}" size="40"/>
-                </div>
-                <div style="clear: both"></div>
-            </div>
-            <div class="form-row">
-                <label>
-                    Info:
-                </label>
-                <div style="float: left; width: 250px; margin-right: 10px;">
-                    <textarea name="info" cols="40" rows="2">${ util.unicodify( data.info ) | h}</textarea>
-                </div>
-                <div style="clear: both"></div>
-            </div>
-            %if trans.get_user() is not None:
-                <div class="form-row">                    
-                    <label>
-                        Annotation / Notes:
-                    </label>
-                    <div style="float: left; width: 250px; margin-right: 10px;">
-                        <textarea name="annotation" cols="40" rows="2">${data_annotation | h}</textarea>
-                    </div>
-                    <div style="clear: both"></div>
-                    <div class="toolParamHelp">Add an annotation or notes to a dataset; annotations are available when a history is viewed.</div>
-                </div>
-            %endif
-            %for name, spec in data.metadata.spec.items():
-                %if spec.visible:
-                    <div class="form-row">
-                        <label>
-                            ${spec.desc}:
-                        </label>
-                        <div style="float: left; width: 250px; margin-right: 10px;">
-                            ${data.metadata.get_html_by_name( name, trans=trans )}
-                        </div>
-                        <div style="clear: both"></div>
-                    </div>
-                %endif
-            %endfor
-            <div class="form-row">
-                <input type="submit" name="save" value="${_('Save')}"/>
-            </div>
-        </form>
-        <form name="auto_detect" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post">
-            <div class="form-row">
-                <div style="float: left; width: 250px; margin-right: 10px;">
-                    <input type="submit" name="detect" value="${_('Auto-detect')}"/>
-                </div>
-                <div class="toolParamHelp" style="clear: both;">
-                    This will inspect the dataset and attempt to correct the above column values if they are not accurate.
-                </div>
-            </div>
-        </form>
-        %if data.missing_meta():
-            <div class="form-row">
-                <div class="errormessagesmall">${_('Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.')}</div>
-            </div>
-        %endif
-    </div>
-</div>
-
-<div class="tab-pane toolForm" id="convert">
-    <div class="toolFormTitle">${_('Convert to new format')}</div>
-    <div class="toolFormBody">
-        <% converters = data.get_converter_types() %>
-        %if len( converters ) > 0:
-            <form name="convert_data" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post">
-                <div class="form-row">
-                    <div style="float: left; width: 250px; margin-right: 10px;">
-                        <select name="target_type">
-                            %for key, value in converters.items():
-                                <option value="${key}">${value.name}</option>
-                            %endfor
-                        </select>
-                    </div>
-                    <div class="toolParamHelp" style="clear: both;">
-                        This will create a new dataset with the contents of this dataset converted to a new format. 
-                    </div>
-                    <div style="clear: both"></div>
-                </div>
-                <div class="form-row">
-                    <input type="submit" name="convert_data" value="${_('Convert')}"/>
-                </div>
-            </form>
-        %else:
-            No conversions available
-        %endif
-    </div>
-</div>
-
-<div class="tab-pane toolForm" id="datatype">
-    <div class="toolFormTitle">${_('Change data type')}</div>
-    <div class="toolFormBody">
-        %if data.datatype.allow_datatype_change:
-            <form name="change_datatype" action="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" method="post">
-                <div class="form-row">
-                    <label>
-                        ${_('New Type')}:
-                    </label>
-                    <div style="float: left; width: 250px; margin-right: 10px;">
-                        ${datatype( data, datatypes )}
-                    </div>
-                    <div class="toolParamHelp" style="clear: both;">
-                        ${_('This will change the datatype of the existing dataset but <i>not</i> modify its contents. Use this if Galaxy has incorrectly guessed the type of your dataset.')}
-                    </div>
-                    <div style="clear: both"></div>
-                </div>
-                <div class="form-row">
-                    <input type="submit" name="change" value="${_('Save')}"/>
-                </div>
-            </form>
-        %else:
-            <div class="form-row">
-                <div class="warningmessagesmall">${_('Changing the datatype of this dataset is not allowed.')}</div>
-            </div>
-        %endif
-    </div>
-</div>
-<p />
-
-<div class="tab-pane" id="permissions">
-%if trans.app.security_agent.can_manage_dataset( current_user_roles, data.dataset ):
-    <%namespace file="/dataset/security_common.mako" import="render_permission_form" />
-    ${render_permission_form( data.dataset, data.get_display_name(), h.url_for( controller='dataset', action='edit', dataset_id=dataset_id ), all_roles )}
-%elif trans.user:
-    <div class="toolForm">
-        <div class="toolFormTitle">View Permissions</div>
-        <div class="toolFormBody">
-            <div class="form-row">
-                %if data.dataset.actions:
-                    <ul>
-                        %for action, roles in trans.app.security_agent.get_permissions( data.dataset ).items():
-                            %if roles:
-                                <li>${action.description}</li>
-                                <ul>
-                                    %for role in roles:
-                                        <li>${role.name}</li>
-                                    %endfor
-                                </ul>
-                            %endif
-                        %endfor
-                    </ul>
-                %else:
-                    <p>This dataset is accessible by everyone (it is public).</p>
-                %endif
-            </div>
-        </div>
-    </div>
-%else:
-    Permissions not available (not logged in)
-%endif
-</div>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/embed.mako
--- a/templates/dataset/embed.mako
+++ /dev/null
@@ -1,19 +0,0 @@
-<%inherit file="/embed_base.mako"/>
-<%!
-    from galaxy.web.framework.helpers import iff
-%>
-
-<%def name="render_item_links( dataset )">
-    <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ), to_ext=dataset.ext )}" title="Save dataset" class="icon-button disk tooltip"></a>
-    ## Links for importing and viewing an item.
-    <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( item.id ) )}" title="Import dataset" class="icon-button import tooltip"></a>
-    <a class="icon-button go-to-full-screen tooltip" href="${h.url_for( controller='/dataset', action='display_by_username_and_slug', username=dataset.history.user.username, slug=trans.security.encode_id( dataset.id ) )}" title="Go to dataset"></a>
-    
-</%def>
-
-<%def name="render_summary_content( dataset, data )">
-##    <ul>
-##        <li>Format : ${dataset.extension}
-##        <pre>${dataset.peek}</pre>
-##    </ul>
-</%def>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/errors.mako
--- a/templates/dataset/errors.mako
+++ /dev/null
@@ -1,80 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
-    <head>
-        <title>Dataset generation errors</title>
-        <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-        <link href="/static/style/base.css" rel="stylesheet" type="text/css" />
-        <style>
-            pre
-            {
-                background: white;
-                color: black;
-                border: dotted black 1px;
-                overflow: auto;
-                padding: 10px;
-            }
-        </style>
-    </head>
-
-    <body>
-        <h2>Dataset generation errors</h2>
-        <p><b>Dataset ${hda.hid}: ${hda.display_name()}</b></p>
-        <% job = hda.creating_job %>
-        %if job:
-            
-            %if job.traceback:
-                The Galaxy framework encountered the following error while attempting to run the tool:
-                <pre>${ util.unicodify( job.traceback ) | h}</pre>
-            %endif
-            %if job.stderr or job.info:
-                Tool execution generated the following error message:
-                %if job.stderr:
-                    <pre>${ util.unicodify( job.stderr ) | h}</pre>
-                %elif job.info:
-                    <pre>${ util.unicodify( job.info ) | h}</pre>
-                %endif
-            %else:
-                Tool execution did not generate any error messages.
-            %endif
-            %if job.stdout:
-                The tool produced the following additional output:
-                <pre>${ util.unicodify( job.stdout ) | h}</pre>
-            %endif
-        %else:
-            The tool did not create any additional job / error info.
-        %endif
-        <%
-            if trans.user:
-                user_email = trans.user.email
-            else:
-                user_email = ''
-        %>
-        <h2>Report this error to the Galaxy Team</h2>
-        <p>
-            The Galaxy team regularly reviews errors that occur in the application. 
-            However, if you would like to provide additional information (such as 
-            what you were trying to do when the error occurred) and a contact e-mail
-            address, we will be better able to investigate your problem and get back
-            to you.
-        </p>
-        <div class="toolForm">
-            <div class="toolFormTitle">Error Report</div>
-            <div class="toolFormBody">
-                <form name="report_error" action="${h.url_for( action='report_error')}" method="post" >
-                    <input type="hidden" name="id" value="${hda.id}" />
-                    <div class="form-row">
-                        <label>Your email</label>
-                        <input type="text" name="email" size="40" value="${user_email}" />
-                    </div>
-                    <div class="form-row">
-                        <label>Message</label>
-                        <textarea name="message" rows="10" cols="40"></textarea>
-                    </div>
-                    <div class="form-row">
-                        <input type="submit" value="Report"/>
-                    </div>
-                </form>
-            </div>
-      </div>
-    </body>
-</html>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/grid.mako
--- a/templates/dataset/grid.mako
+++ /dev/null
@@ -1,1 +0,0 @@
-<%inherit file="/grid_base.mako"/>
\ No newline at end of file

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/item_content.mako
--- a/templates/dataset/item_content.mako
+++ /dev/null
@@ -1,3 +0,0 @@
-<%namespace file="/dataset/display.mako" import="*" />
-
-${render_item( item, item_data )}
\ No newline at end of file

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/large_file.mako
--- a/templates/dataset/large_file.mako
+++ /dev/null
@@ -1,11 +0,0 @@
-<%inherit file="/base.mako"/>
-
-<div class="warningmessagelarge">
-    This dataset is large and only the first megabyte is shown below.<br />
-    <a href="${h.url_for( controller='dataset', action='display', dataset_id=trans.security.encode_id( data.id ), filename='' )}">Show all</a> |
-    <a href="${h.url_for( controller='dataset', action='display', dataset_id=trans.security.encode_id( data.id ), to_ext=data.ext )}">Save</a>
-</div>
-
-<pre>
-${ unicode( truncated_data, 'utf-8' ) | h }
-</pre>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/security_common.mako
--- a/templates/dataset/security_common.mako
+++ /dev/null
@@ -1,130 +0,0 @@
-<%def name="render_select( current_actions, action_key, action, roles )">
-    <%
-        import sets
-        in_roles = sets.Set()
-        for a in current_actions:
-            if a.action == action.action:
-                in_roles.add( a.role )
-        out_roles = filter( lambda x: x not in in_roles, roles )
-    %>
-    <p>
-        <b>${action.action}:</b> ${action.description}
-        %if action == trans.app.security_agent.permitted_actions.DATASET_ACCESS:
-            <br/>
-            NOTE: Users must have every role associated with this dataset in order to access it
-        %endif
-    </p>
-    <div style="width: 100%; white-space: nowrap;">
-        <div style="float: left; width: 50%;">
-            Roles associated:<br />
-            <select name="${action_key}_in" id="${action_key}_in_select" class="in_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple>
-                %for role in in_roles:
-                    <option value="${role.id}">${role.name}</option>
-                %endfor
-            </select><br />
-            <div style="width: 98%; text-align: right"><input type="submit" id="${action_key}_remove_button" class="role_remove_button" value=">>"/></div>
-        </div>
-        <div style="width: 50%;">
-            Roles not associated:<br />
-            <select name="${action_key}_out" id="${action_key}_out_select" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple>
-                %for role in out_roles:
-                    <option value="${role.id}">${role.name}</option>
-                %endfor
-            </select><br />
-            <input type="submit" id="${action_key}_add_button" class="role_add_button" value="<<"/>
-        </div>
-    </div>
-</%def>
-
-## Any permission ( e.g., 'DATASET_ACCESS' ) included in the do_not_render param will not be rendered on the page.
-<%def name="render_permission_form( obj, obj_name, form_url, roles, do_not_render=[], all_roles=[] )">
-    <%
-        if isinstance( obj, trans.app.model.User ):
-            current_actions = obj.default_permissions
-            permitted_actions = trans.app.model.Dataset.permitted_actions.items()
-            obj_str = 'user %s' % obj_name
-            obj_type = 'dataset'
-        elif isinstance( obj, trans.app.model.History ):
-            current_actions = obj.default_permissions
-            permitted_actions = trans.app.model.Dataset.permitted_actions.items()
-            obj_str = 'history %s' % obj_name
-            obj_type = 'dataset'
-        elif isinstance( obj, trans.app.model.Dataset ):
-            current_actions = obj.actions
-            permitted_actions = trans.app.model.Dataset.permitted_actions.items()
-            obj_str = obj_name
-            obj_type = 'dataset'
-        elif isinstance( obj, trans.app.model.LibraryDatasetDatasetAssociation ):
-            current_actions = obj.actions + obj.dataset.actions
-            permitted_actions = trans.app.model.Dataset.permitted_actions.items() + trans.app.model.Library.permitted_actions.items()
-            obj_str = obj_name
-            obj_type = 'dataset'
-        elif isinstance( obj, trans.app.model.Library ):
-            current_actions = obj.actions
-            permitted_actions = trans.app.model.Library.permitted_actions.items()
-            obj_str = 'library %s' % obj_name
-            obj_type = 'library'
-        elif isinstance( obj, trans.app.model.LibraryDataset ):
-            current_actions = obj.actions
-            permitted_actions = trans.app.model.Library.permitted_actions.items()
-            obj_str = 'library dataset %s' % obj_name
-            obj_type = 'library'
-        elif isinstance( obj, trans.app.model.LibraryFolder ):
-            current_actions = obj.actions
-            permitted_actions = trans.app.model.Library.permitted_actions.items()
-            obj_str = 'library folder %s' % obj_name
-            obj_type = 'library'
-        else:
-            current_actions = []
-            permitted_actions = {}.items()
-            obj_str = 'unknown object %s' %obj_name
-            obj_type = ''
-    %>
-    <script type="text/javascript">
-        $( document ).ready( function () {
-            $( '.role_add_button' ).click( function() {
-                var action = this.id.substring( 0, this.id.lastIndexOf( '_add_button' ) )
-                var in_select = '#' + action + '_in_select';
-                var out_select = '#' + action + '_out_select';
-                return !$( out_select + ' option:selected' ).remove().appendTo( in_select );
-            });
-            $( '.role_remove_button' ).click( function() {
-                var action = this.id.substring( 0, this.id.lastIndexOf( '_remove_button' ) )
-                var in_select = '#' + action + '_in_select';
-                var out_select = '#' + action + '_out_select';
-                return !$( in_select + ' option:selected' ).remove().appendTo( out_select );
-            });
-            $( 'form#edit_role_associations' ).submit( function() {
-                $( '.in_select option' ).each(function( i ) {
-                    $( this ).attr( "selected", "selected" );
-                });
-            });
-        });
-    </script>
-    <div class="toolForm">
-        <div class="toolFormTitle">Manage ${obj_type} permissions on ${obj_str}</div>
-        <div class="toolFormBody">
-            <form name="edit_role_associations" id="edit_role_associations" action="${form_url}" method="post">
-                <div class="form-row"></div>
-                %for k, v in permitted_actions:
-                    %if k not in do_not_render:
-                        <div class="form-row">
-                            ## LIBRARY_ACCESS is a special case because we need to render all roles instead of
-                            ## roles derived from the roles associated with LIBRARY_ACCESS.
-                            <% render_all_roles = k == 'LIBRARY_ACCESS' %>
-                            %if render_all_roles:
-                                ${render_select( current_actions, k, v, all_roles )}
-                            %else:
-                                ${render_select( current_actions, k, v, roles )}
-                            %endif
-                        </div>
-                    %endif
-                %endfor
-                <div class="form-row">
-                    <input type="submit" name="update_roles_button" value="Save"/>
-                </div>
-            </form>
-        </div>
-    </div>
-    <p/>
-</%def>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/dataset/tabular_chunked.mako
--- a/templates/dataset/tabular_chunked.mako
+++ /dev/null
@@ -1,103 +0,0 @@
-<%inherit file="/base.mako"/>
-
-
-<%def name="title()">Dataset Display</%def>
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-    <script type="text/javascript">
-        var DATASET_URL   = "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( dataset.id ))}";
-        var COLUMN_NUMBER  = ${column_number};
-        var COLUMN_TYPES = ${column_types};
-        var COLUMN_NAMES = ${column_names};
-
-        var chunk = ${chunk};
-        var current_chunk = 0;
-
-        function renderCell(cell_contents, index, colspan){
-            if (colspan !== undefined){
-                return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents);
-            }
-            else if (COLUMN_TYPES[index] == 'str' || COLUMN_TYPES[index] == 'list'){
-                /* Left align all str columns, right align the rest */
-                return $('<td>').addClass('stringalign').text(cell_contents);;
-            }
-            else{
-                return $('<td>').text(cell_contents);
-            }
-        }
-
-        function renderRow(line){
-            /* Check length of cells to ensure this is a complete row. */
-            var cells = line.split('\t');
-            var row = $('<tr>');
-            if (cells.length == COLUMN_NUMBER){
-                $.each(cells, function(index, cell_contents){
-                    row.append(renderCell(cell_contents, index));
-                });
-            }
-            else if(cells.length > COLUMN_NUMBER){
-                /* SAM file or like format with optional metadata included */
-                $.each(cells.slice(0, COLUMN_NUMBER -1), function(index, cell_contents){
-                    row.append(renderCell(cell_contents, index));
-                });
-                row.append(renderCell(cells.slice(COLUMN_NUMBER -1).join('\t'), COLUMN_NUMBER-1));
-            }
-            else if(COLUMN_NUMBER > 5 && cells.length == COLUMN_NUMBER - 1 ){
-                /* SAM file or like format with optional metadata missing */
-                $.each(cells, function(index, cell_contents){
-                    row.append(renderCell(cell_contents, index));
-                });
-                row.append($('<td>'));
-            }
-            else{
-                /* Comment line, just return the one cell*/
-                row.append(renderCell(line, 0, COLUMN_NUMBER));
-            }
-            return row;
-        }
-
-        function renderChunk(chunk){
-            var table = $('#content_table');
-            if (chunk.ck_data == ""){
-                current_chunk = -1;
-            }
-            else if(chunk.ck_index === current_chunk + 1){
-                if (current_chunk === 0 && COLUMN_NAMES){
-                    table.append('<tr><th>' + COLUMN_NAMES.join('</th><th>') + '</th></tr>');
-                }
-                var lines = chunk.ck_data.split('\n');
-                $.each(lines, function(index, line){
-                    table.append(renderRow(line));
-                });
-                current_chunk = chunk.ck_index;
-            }
-        }
-
-        $(document).ready(function(){
-            renderChunk(chunk);
-            $(window).scroll(function(){
-                if ($(window).scrollTop() == $(document).height() - $(window).height()){
-                    if (current_chunk !== -1){
-                        $.getJSON(DATASET_URL,
-                                  {chunk: current_chunk},
-                                  function(result){renderChunk(result)});
-                    }
-                }
-            });
-            $('#loading_indicator').ajaxStart(function(){
-               $(this).show();
-            }).ajaxStop(function(){
-               $(this).hide();
-            });
-        });
-    </script>
-</%def>
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-</%def>
-
-<div id="loading_indicator" ></div>
-<table id="content_table" cellpadding="0">
-</table>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/copy.mako
--- a/templates/history/copy.mako
+++ /dev/null
@@ -1,27 +0,0 @@
-<% _=n_ %>
-<%inherit file="/base.mako"/>
-<%def name="title()">Copy History</%def>
-
-<div class="toolForm">
-  <div class="toolFormTitle">Copy History</div>
-    <div class="toolFormBody">
-        <form action="${h.url_for( controller='history', action='copy' )}" method="post" >
-            <div class="form-row">
-                %if id_argument is not None:
-                  <input type="hidden" name="id" value="${id_argument}">
-                %endif
-                You can make a copy of the history that includes all datasets in the original history or just the active 
-                (not deleted) datasets.
-            </div>
-            <div class="form-row">
-                <input type="radio" name="copy_choice" value="activatable"> Copy all datasets, including deleted ones
-            </div>
-            <div class="form-row">
-                <input type="radio" name="copy_choice" value="active"> Copy only active (not deleted) datasets
-            </div>
-            <div class="form-row">
-                <input type="submit" name="copy_choice_button" value="Copy">
-            </div>
-        </form>
-    </div>
-</div>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/display.mako
--- a/templates/history/display.mako
+++ /dev/null
@@ -1,84 +0,0 @@
-<%inherit file="/display_base.mako"/>
-<%namespace file="/root/history_common.mako" import="render_dataset" />
-
-## Set vars so that there's no need to change the code below.
-<% 
-    history = published_item 
-    datasets = published_item_data
-%>
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-</%def>
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "history" )}
-    <style type="text/css">
-        .historyItemBody {
-            display: none;
-        }
-        .column {
-            float: left;
-            padding: 10px;
-            margin: 20px;
-            background: #666;
-            border: 5px solid #ccc;
-            width: 300px;
-        }
-    </style>
-
-    <noscript>
-        <style>
-            .historyItemBody {
-                display: block;
-            }
-        </style>
-    </noscript>
-</%def>
-
-<%def name="render_item_links( history )">
-    <a 
-        href="${h.url_for( controller='/history', action='imp', id=trans.security.encode_id(history.id) )}"
-        class="icon-button import"
-        ## Needed to overwide initial width so that link is floated left appropriately.
-        style="width: 100%"
-        title="Import history">Import history</a>
-</%def>
-
-<%def name="render_item( history, datasets )">
-    %if history.deleted:
-        <div class="warningmessagesmall">
-            ${_('You are currently viewing a deleted history!')}
-        </div>
-        <p></p>
-    %endif
-
-    %if not datasets:
-        <div class="infomessagesmall" id="emptyHistoryMessage">
-    %else:    
-        ## Render requested datasets, ordered from newest to oldest, including annotations.
-        <table class="annotated-item">
-            <tr><th>Dataset</th><th class="annotation">Annotation</th></tr>
-            %for data in datasets:
-                <tr>
-                    %if data.visible:
-                        <td>
-                            <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}">
-                                ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )}
-                            </div>
-                        </td>
-                        <td class="annotation">
-                        %if hasattr( data, "annotation") and data.annotation is not None:
-                            ${data.annotation}
-                        %endif
-                        </td>
-                    %endif
-                </tr>
-            %endfor
-        </table>
-        <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;">
-    %endif
-            ${_("This history is empty.")}
-        </div>
-</%def>
\ No newline at end of file

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/display_structured.mako
--- a/templates/history/display_structured.mako
+++ /dev/null
@@ -1,132 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/root/history_common.mako" import="render_dataset" />
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "history" )}
-    <style type="text/css">
-        body {
-            background: white;
-            padding: 5px;
-        }
-        
-        .clickable {
-            cursor: pointer;
-        }
-        
-        .workflow {
-            border: solid gray 1px;
-            margin: 5px 0;
-            border-left-width: 5px;
-        }
-        
-        .workflow > .header {
-            background: lightgray;
-            padding: 5px 10px;
-            
-            font-weight: bold;
-        }
-        
-        .workflow > .body {
-            border-top: solid gray 1px;
-            padding: 5px;
-        }
-        
-        div.toolForm {
-            margin: 5px 0;
-            border-left-width: 5px;
-        }
-        div.toolFormBody {
-            padding: 5px 5px;
-        }
-    </style>
-</%def>
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-    <script type="text/javascript">
-        $(function(){
-            
-            $(".workflow, .tool").each( function() {
-                var body = $(this).children( ".body" );
-                $(this).children( ".header" ).click( function() {
-                    body.toggle();
-                }).addClass( "clickable" );
-                // body.hide();
-            });
-            
-            $(".historyItem").each( function() {
-                var id = this.id;
-                var body = $(this).children( "div.historyItemBody" );
-                var peek = body.find( "pre.peek" )
-                $(this).children( ".historyItemTitleBar" ).find( ".historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() {
-                    if ( body.is(":visible") ) {
-                        // Hiding stuff here
-                        if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ) }
-                        body.slideUp( "fast" );
-                    } else {
-                        // Showing stuff here
-                        body.slideDown( "fast", function() { 
-                            if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); } 
-                        });
-                    }
-                    return false;
-                });
-                body.hide();
-            });
-        });    
-    </script>
-</%def>
-
-<%def name="render_item( entity, children )">
-<%
-entity_name = entity.__class__.__name__
-if entity_name == "HistoryDatasetAssociation":
-    render_item_hda( entity, children )
-elif entity_name == "Job":
-    render_item_job( entity, children )
-elif entity_name == "WorkflowInvocation":
-    render_item_wf( entity, children )
-%>
-</%def>
-
-<%def name="render_item_hda( hda, children  )">
-    ${render_dataset( hda, hda.hid, display_structured=True )}
-</%def>
-
-<%def name="render_item_job( job, children  )">
-
-    <div class="tool toolForm">
-        <%
-            tool = trans.app.toolbox.get_tool( job.tool_id )
-            if tool:
-                tool_name = tool.name
-            else:
-                tool_name = "Unknown tool with id '%s'" % job.tool_id       
-        %>
-        <div class="header toolFormTitle">Tool: ${tool_name}</div>
-        <div class="body toolFormBody">
-        %for e, c in reversed( children ):
-            ${render_item( e, c )}
-        %endfor
-        </div>
-    </div>
-
-</%def>
-
-<%def name="render_item_wf( wf, children )">
-
-    <div class="workflow">
-        <div class="header">Workflow: ${wf.workflow.name}</div>
-        <div class="body">
-        %for e, c in reversed( children ):
-            ${render_item( e, c )}
-        %endfor
-        </div>
-    </div>
-
-</%def>
-
-%for entity, children in items:
-    ${render_item( entity, children )}
-%endfor
\ No newline at end of file

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/embed.mako
--- a/templates/history/embed.mako
+++ /dev/null
@@ -1,13 +0,0 @@
-<%inherit file="/embed_base.mako"/>
-<%!
-    from galaxy.web.framework.helpers import iff
-%>
-
-<%def name="render_summary_content( history, datasets )">
-
-##    <ul>
-##        <% num_datasets = len ( datasets ) %>
-##        <li>${num_datasets} dataset${iff( num_datasets != 1, "s", "" )}
-##        <li>Operations: ...
-##    </ul>
-</%def>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/grid.mako
--- a/templates/history/grid.mako
+++ /dev/null
@@ -1,25 +0,0 @@
-<%inherit file="../grid_base.mako"/>
-
-<%def name="grid_javascripts()">
-    ${parent.grid_javascripts()}
-    <script type="text/javascript">
-        %if refresh_frames:
-            %if 'history' in refresh_frames:
-                if ( parent.frames && parent.frames.galaxy_history ) {
-                    parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}";
-                    if ( parent.force_right_panel ) {
-                        parent.force_right_panel( 'show' );
-                    }
-                }
-            %endif
-        %endif
-    </script>
-</%def>
-
-<%def name="grid_body( grid )">
-    ${self.make_grid( grid )}
-    <br/>
-    <div class="toolParamHelp" style="clear: both;">
-        Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted.
-    </div>
-</%def>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/item_content.mako
--- a/templates/history/item_content.mako
+++ /dev/null
@@ -1,3 +0,0 @@
-<%namespace file="/history/display.mako" import="*" />
-
-${render_item( item, item_data )}
\ No newline at end of file

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/list_as_xml.mako
--- a/templates/history/list_as_xml.mako
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0"?>
-<history_ids>
-  %for i, history in enumerate( t.user.histories ):
-    <data id="${trans.security.encode_id( history.id )}" hid="${i+1}" num="${len(history.datasets)}" name="${history.name}" create="${history.create_time}" update="${history.update_time}" >
-    </data>
-  %endfor
-</history_ids>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/list_published.mako
--- a/templates/history/list_published.mako
+++ /dev/null
@@ -1,34 +0,0 @@
-<%inherit file="/webapps/galaxy/base_panels.mako"/>
-
-<%def name="init()">
-<%
-    self.has_left_panel=False
-    self.has_right_panel=False
-    self.active_view="shared"
-    self.message_box_visible=False
-%>
-</%def>
-
-<%def name="title()">
-    Galaxy | Published Histories
-</%def>
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    <style>
-        .grid td {
-            min-width: 100px;
-        }
-    </style>
-</%def>
-
-<%def name="center_panel()">
-
-    <div style="overflow: auto; height: 100%;">
-        <div class="page-container" style="padding: 10px;">
-            ${h.to_unicode( grid )}
-        </div>
-    </div>
-
-
-</%def>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/options.mako
--- a/templates/history/options.mako
+++ /dev/null
@@ -1,32 +0,0 @@
-<% _=n_ %>
-<%inherit file="/base.mako"/>
-<%def name="title()">History options</%def>
-    
-<h2>${_('History Options')}</h2>
-
-%if not user:
-<div class="infomessage">
-    <div>${_('You must be ')}<a target="galaxy_main" href="${h.url_for( controller='user', action='login' )}">${_('logged in')}</a>${_(' to store or switch histories.')}</div>
-</div>
-%endif
-
-<ul>
-    %if user:
-        <li><a href="${h.url_for( controller='history', action='list')}" target="galaxy_main">Previously</a> stored histories</li>
-        %if len( history.active_datasets ) > 0:
-            <li><a href="${h.url_for( controller='root', action='history_new' )}">Create</a> a new empty history</li>
-            <li><a href="${h.url_for( controller='workflow', action='build_from_current_history' )}">Construct workflow</a> from current history</li>
-            <li><a href="${h.url_for( controller='history', action='copy', id=trans.security.encode_id( history.id ) )}">Copy</a> current history</li>
-        %endif
-        <li><a href="${h.url_for( controller='history', action='share' )}" target="galaxy_main">Share</a> current history</div>
-        <li><a href="${h.url_for( controller='root', action='history_set_default_permissions' )}">Change default permissions</a> for current history</li>
-    %endif
-    %if len( history.activatable_datasets ) > 0:
-        <li><a href="${h.url_for( controller='root', action='history', show_deleted=True)}" target="galaxy_history">Show deleted</a> datasets in current history</li>
-    %endif
-    <li><a href="${h.url_for( controller='history', action='rename', id=trans.security.encode_id( history.id ) )}" target="galaxy_main">Rename</a> current history (stored as "${history.name}")</li>
-    <li><a href="${h.url_for( controller='history', action='delete_current' )}" confirm="Are you sure you want to delete the current history?">Delete</a> current history</div>
-    %if user and user.histories_shared_by_others:
-        <li><a href="${h.url_for( controller='history', action='list_shared')}" target="galaxy_main">Histories</a> shared with you by others</li>
-    %endif
-</ul>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/permissions.mako
--- a/templates/history/permissions.mako
+++ /dev/null
@@ -1,8 +0,0 @@
-<%inherit file="/base.mako"/>
-<%def name="title()">Change Default Permissions on New Datasets in This History</%def>
-<%namespace file="/dataset/security_common.mako" import="render_permission_form" />
-
-%if trans.user:
-    <% history = trans.get_history() %>
-    ${render_permission_form( history, history.name, h.url_for(), trans.user.all_roles() )}
-%endif

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/rename.mako
--- a/templates/history/rename.mako
+++ /dev/null
@@ -1,38 +0,0 @@
-<%inherit file="/base.mako"/>
-<%def name="title()">${_('Rename History')}</%def>
-
-<div class="toolForm">
-  <div class="toolFormTitle">${_('Rename')}</div>
-    <div class="toolFormBody">
-        <form action="${h.url_for( controller='history', action='rename' )}" method="post" >
-            <div class="form-row">
-            <table>
-                <thead>
-                    <tr>
-                        <th>${_('Current Name')}</th>
-                        <th>${_('New Name')}</th>
-                    </tr>
-                </thead>
-                <tbody>
-                %for history in histories:
-                    <tr>
-                        <td>
-                            <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}">
-                            ${history.get_display_name() | h}
-                        </td>
-                        <td>
-                            <input type="text" name="name" value="${history.get_display_name() | h}" size="40">
-                        </td>
-                    </tr>
-                %endfor
-                </tbody>
-                <tr>
-                    <td colspan="2">
-                        <input type="submit" name="history_rename_btn" value="${_('Rename Histories')}">
-                    </td>
-                </tr>
-            </table>
-            </div>
-        </form>
-    </div>
-</div>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/share.mako
--- a/templates/history/share.mako
+++ /dev/null
@@ -1,192 +0,0 @@
-<% _=n_ %>
-<%inherit file="/base.mako"/>
-<%def name="title()">Share histories</%def>
-
-<div class="toolForm">
-    <div class="toolFormTitle">Share ${len( histories)} histories</div>
-    <div class="toolFormBody">
-        %if not can_change and not cannot_change and not no_change_needed:
-            ## We are sharing histories that contain only public datasets
-            <form name='share' id='share' action="${h.url_for( action='share' )}" method="post" >
-                <div class="form-title-row"><b>Histories to be shared:</b></div>
-                <div class="form-row" style="padding-left: 2em;">
-                    <table width="100%">
-                        <thead>
-                            <th>${_('History Name')}</th>
-                            <th>${_('Number of Datasets')}</th>
-                        </thead>
-                        <tbody>
-                            %for history in histories:
-                                <tr>
-                                    <td>
-                                        <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}">
-                                        ${ util.unicodify( history.name )}
-                                    </td>
-                                    <td>
-                                        %if len( history.datasets ) < 1:
-                                            <div class="warningmark">${_('This history contains no data.')}</div>
-                                        %else:
-                                            ${len(history.datasets)}
-                                        %endif
-                                    </td>
-                                </tr>
-                            %endfor
-                        </tbody>
-                    </table>
-                </div>
-                <div style="clear: both"></div>
-                <div class="form-row">
-                    <label>Galaxy user emails with which to share histories</label>
-                    <div style="float: left; width: 250px; margin-right: 10px;">
-                        <input type="text" name="email" value="${email}" size="40">
-                    </div>
-                    <div class="toolParamHelp" style="clear: both;">
-                        Enter a Galaxy user email address or a comma-separated list of addresses if sharing with multiple users
-                    </div>
-                </div>
-                %if send_to_err:
-                    <div style="clear: both"></div>
-                    <div class="form-row">
-                        <div class="errormessage">${send_to_err}</div>
-                    </div>
-                %endif
-                <div style="clear: both"></div>
-                <div class="form-row">
-                    <input type="submit" name="share_button" value="Submit">
-                </div>
-            </form>
-        %else:
-            ## We are sharing restricted histories
-            %if no_change_needed or can_change:
-                <form name='share_restricted' id=share_restricted' action="${h.url_for( controller='history', action='share_restricted' )}" method="post">
-                    %if send_to_err:
-                        <div style="clear: both"></div>
-                        <div class="form-row">
-                            <div class="errormessage">${send_to_err}</div>
-                        </div>
-                    %endif
-                    ## Needed for rebuilding dicts
-                    <input type="hidden" name="email" value="${email}" size="40">
-                    %for history in histories:
-                        <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}">
-                    %endfor
-                    %if no_change_needed:
-                        ## no_change_needed looks like: {historyX : [hda, hda], historyY : [hda] }
-                        <div style="clear: both"></div>
-                        <div class="form-row">
-                            <div class="donemessage">
-                                The following datasets can be shared with ${email} with no changes
-                            </div>
-                        </div>                        
-                        %for history, hdas in no_change_needed.items():
-                            <div class="form-row">
-                                <label>History</label>
-                                ${util.unicodify( history.name )}
-                            </div>
-                            <div style="clear: both"></div>
-                            <div class="form-row">
-                                <label>Datasets</label>
-                            </div>
-                            %for hda in hdas:
-                                <div class="form-row">
-                                    ${util.unicodify( hda.name )}
-                                    %if hda.deleted:
-                                        (deleted)
-                                    %endif
-                                </div>
-                            %endfor
-                        %endfor
-                    %endif
-                    %if can_change:
-                        ## can_change looks like: {historyX : [hda, hda], historyY : [hda] }
-                        <div style="clear: both"></div>
-                        <div class="form-row">
-                            <div class="warningmessage">
-                                The following datasets can be shared with ${email} by updating their permissions
-                            </div>
-                        </div>
-                        %for history, hdas in can_change.items():
-                            <div class="form-row">
-                                <label>History</label>
-                                ${util.unicodify( history.name )}
-                            </div>
-                            <div style="clear: both"></div>
-                            <div class="form-row">
-                                <label>Datasets</label>
-                            </div>
-                            %for hda in hdas:
-                                <div class="form-row">
-                                    ${util.unicodify( hda.name )}
-                                    %if hda.deleted:
-                                        (deleted)
-                                    %endif
-                                </div>
-                            %endfor
-                        %endfor
-                    %endif
-                    %if cannot_change:
-                        ## cannot_change looks like: {historyX : [hda, hda], historyY : [hda] }
-                        <div style="clear: both"></div>
-                        <div class="form-row">
-                            <div class="errormessage">
-                                The following datasets cannot be shared with ${email} because you are not authorized to 
-                                change the permissions on them
-                            </div>
-                        </div>
-                        %for history, hdas in cannot_change.items():
-                            <div class="form-row">
-                                <label>History</label>
-                                ${util.unicodify( history.name )}
-                            </div>
-                            <div style="clear: both"></div>
-                            <div class="form-row">
-                                <label>Datasets</label>
-                            </div>
-                            %for hda in hdas:
-                                <div class="form-row">
-                                    ${util.unicodify( hda.name )}
-                                    %if hda.deleted:
-                                        (deleted)
-                                    %endif
-                                </div>
-                            %endfor
-                        %endfor
-                    %endif
-                    <div class="toolFormTitle"></div>
-                    <div class="form-row">
-                        <label>How would you like to proceed?</label>
-                    </div>
-                    %if can_change:
-                        <div class="form-row">
-                            <input type="radio" name="action" value="public"> Make datasets public so anyone can access them 
-                            %if cannot_change:
-                                (where possible)
-                            %endif
-                        </div>
-                        <div class="form-row">
-                            %if no_change_needed:
-                                <input type="radio" name="action" value="private"> Make datasets private to me and the user(s) with whom I am sharing
-                            %else:
-                                <input type="radio" name="action" value="private" checked> Make datasets private to me and the user(s) with whom I am sharing
-                            %endif
-                            %if cannot_change:
-                                (where possible)
-                            %endif
-                        </div>
-                    %endif
-                    %if no_change_needed:
-                        <div class="form-row">
-                            <input type="radio" name="action" value="share_anyway" checked> Share anyway
-                            %if can_change:
-                                (don't change any permissions)
-                            %endif
-                        </div>
-                    %endif
-                    <div class="form-row">
-                        <input type="submit" name="share_restricted_button" value="Go"><br/>
-                    </div>
-                </form>
-            %endif
-        %endif
-    </div>
-</div>

diff -r c714feaad11541377edd84af1179869c1a8e4f47 -r 4c6e63dc04c9bd2a82ecd11b8ffdf5b544a8e355 templates/history/view.mako
--- a/templates/history/view.mako
+++ /dev/null
@@ -1,140 +0,0 @@
-<%namespace file="/display_common.mako" import="get_history_link, get_controller_name" />
-<%namespace file="/root/history_common.mako" import="render_dataset" />
-<%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" />
-
-<%!
-    def inherit(context):
-        if context.get('use_panels'):
-            return '/webapps/galaxy/base_panels.mako'
-        else:
-            return '/base.mako'
-%>
-<%inherit file="${inherit(context)}"/>
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-    ${h.js( "libs/jquery/jstorage" )}
-    <script type="text/javascript">
-        $(function() {
-            init_history_items( $("div.historyItemWrapper"), false, "nochanges" );
-        });
-    </script>
-</%def>
-
-<%def name="stylesheets()">
-    ${parent.stylesheets()}
-    ${h.css( "history", "autocomplete_tagging" )}
-    <style type="text/css">
-        .historyItemContainer {
-          padding-right: 3px;
-          border-right-style: solid;
-          border-right-color: #66AA66;
-        }
-        .page-body
-        {
-            padding: 10px;
-            float: left;
-            width: 65%;
-        }
-        .page-meta
-        {
-            float: right;
-            width: 27%;
-            padding: 0.5em;
-            margin: 0.25em;
-            vertical-align: text-top;
-            border: 2px solid #DDDDDD;
-            border-top: 4px solid #DDDDDD;
-        }
-    </style>
-
-    <style>
-        .historyItemBody {
-            display: none;
-        }
-    </style>
-
-    <noscript>
-        <style>
-            .historyItemBody {
-                display: block;
-            }
-        </style>
-    </noscript>
-</%def>
-
-<%def name="init()">
-<%
-    self.has_left_panel=False
-    self.has_right_panel=False
-    self.message_box_visible=False
-%>
-</%def>
-
-<%def name="body()">
-    ${center_panel()}
-</%def>
-
-<%def name="center_panel()">
-    ## Get URL to other histories owned by user that owns this history.
-    <%
-        ##TODO: is there a better way to create this URL? Can't use 'f-username' as a key b/c it's not a valid identifier.
-        href_to_published_histories = h.url_for( controller='/history', action='list_published')
-        if history.user is not None:
-            href_to_user_histories = h.url_for( controller='/history', action='list_published', xxx=history.user.username).replace( 'xxx', 'f-username')
-        else:
-            href_to_user_histories = h.url_for( controller='/history', action='list_published' )##should this instead be be None or empty string?
-    %>
-    
-    <div class="unified-panel-header" unselectable="on">
-    </div>
-    
-    <div class="unified-panel-body">
-        <div style="overflow: auto; height: 100%;">
-            ## Render view of history.
-            <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px">
-                %if not history.purged:
-                    <a href="${h.url_for( action='imp', id=trans.security.encode_id(history.id) )}">import and start using history</a> |
-                    <a href="${get_history_link( history )}">${_('refresh')}</a> |
-                %endif
-                %if show_deleted:
-                    <a href="${h.url_for( id=trans.security.encode_id(history.id), show_deleted=False, use_panels=use_panels )}">${_('hide deleted')}</a> |
-                %else:
-                    <a href="${h.url_for( id=trans.security.encode_id(history.id), show_deleted=True, use_panels=use_panels )}">${_('show deleted')}</a> |
-                %endif
-                <a href="#" class="toggle">collapse all</a>
-            </div>
-
-            <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px">
-                <div id="history-name">${history.get_display_name()}</div>
-            </div>
-
-            %if history.deleted:
-                <div class="warningmessagesmall">
-                    ${_('You are currently viewing a deleted history!')}
-                </div>
-                <p></p>
-            %endif
-
-            %if not datasets:
-
-                <div class="infomessagesmall" id="emptyHistoryMessage">
-
-            %else:    
-
-                ## Render requested datasets, ordered from newest to oldest
-                %for data in datasets:
-                    %if data.visible:
-                        <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}">
-                            ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )}
-                        </div>
-                    %endif
-                %endfor
-
-                <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;">
-            %endif
-                    ${_("Your history is empty. Click 'Get Data' on the left pane to start")}
-                </div>
-        </div>
-    </div>
-</%def>

This diff is so big that we needed to truncate the remainder.

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: james_taylor: template: Move templates used *only* by the galaxy webapp into templates/webapps/galaxy

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[galaxy-commits] commit/galaxy-central: james_taylor: template: Move templates used only by the galaxy webapp into templates/webapps/galaxy